Rapid mass spectrometric conversion of tissue biopsy samples into permanent quantitative digital proteome maps
Open accessAbstract
Clinical specimens are each inherently unique, limited and nonrenewable. Small samples such as tissue biopsies are often completely consumed after a limited number of analyses. Here we present a method that enables fast and reproducible conversion of a small amount of tissue (approximating the quantity obtained by a biopsy) into a single, permanent digital file representing the mass spectrometry (MS)-measurable proteome of the sample. The method combines pressure cycling technology (PCT) and sequential window acquisition of all theoretical fragment ion spectra (SWATH)-MS. The resulting proteome maps can be analyzed, re-analyzed, compared and mined in silico to detect and quantify specific proteins across multiple samples. We used this method to process and convert 18 biopsy samples from nine patients with renal cell carcinoma into SWATH-MS fragment ion maps. From these proteome maps we detected and quantified more than 2,000 proteins with a high degree of reproducibility across all samples. The measured proteins clearly distinguished tumorous kidney tissues from healthy tissues and differentiated distinct histomorphological kidney cancer subtypes.
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SWATH-MS and related DIA approaches have achieved high intra-laboratory reproducibility in a variety of research questions.
“SWATH-MS and related DIA approaches have achieved a high degree of reproducibility in intra-laboratory studies in a variety of research questions such as interaction proteomics40, 41, plasma proteomics42, tissue proteomics43, microbial proteomics44, 45, pre-clinical toxicology9, analysis of genetic reference strains46, and many others.”
From Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry (2017) · cites this paper as [43]
The result of this study, focused on assessing variation in data acquisition, is paralleled by concurrent improvements in robustness of data analysis tools, methods for error rate control, and sample preparation techniques.
“The result of our study, focused on assessing variation in data acquisition, is paralleled by concurrent improvements in the robustness of data analysis tools39, methods for error rate control55, and sample preparation techniques43.”
From Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry (2017) · cites this paper as [43]
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- Authors
- Guo, T., Kouvonen, P., Koh, C. C., Gillet, L. C., Wolski, W. E., Röst, H. L., Rosenberger, G., Collins, B. C., Blum, L. C., Gillessen, S., Joerger, M., Jochum, W., & Aebersold, R.
- Affiliations
- ETH Zurich (CH)
- Åbo Akademi University (FI)
- Heidelberg University (DE)
- University of Zurich (CH)
- Kantonsspital St. Gallen (CH)
- Corresponding author
- Aebersold, Ruedi
- ORCID
- Venue
- Nature Medicine
- Published
- 2015-03-02
- Volume
- 21
- Issue
- 4
- Pages
- 407-413
- ISSN
- 1078-8956 (ISSN-L)
- 1546-170X
- PMC
- PMC4390165
- OpenAlex
- W2033047611
- Cited by
- 376
- References
- 39
- Citations by year
- 2026: 12 · 2025: 18 · 2024: 20 · 2023: 38 · 2022: 36 · 2021: 39 · 2020: 52 · 2019: 37 · 2018: 31 · 2017: 37 · 2016: 37 · 2015: 19
- FWCI
- 18.58
- Type
- journal article
- Language
- en
- Open access
- green
- pure.qub.ac.uk
- Licence
- Locations
- Nature Medicine (publishedVersion)
- PubMed (publishedVersion)
- Research Portal (Queen's University Belfast) (publishedVersion, other-oa)
- PubMed Central (acceptedVersion)
- Research Explorer (The University of Manchester) (submittedVersion)
- Funders
- Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (107679, 3100A0)
- Suomen Kulttuurirahasto
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Metabolomics and Mass Spectrometry Studies
- Keywords
- tissue biopsy, proteome mapping, SWATH-MS, renal cell carcinoma, protein quantification
- MeSH terms
- Biopsy, Carcinoma, Renal Cell, Humans, Ions, Kidney, Kidney Neoplasms, Peptides, Pressure, Mass Spectrometry, Reproducibility of Results, Proteome, Proteomics
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